@Cesar-Vargas Looking at the code of /usr/bin/arduino-dock in the arduino-dock-2 package it looks like the flash bootloader command is not supported. The code actually tried to open a file called bootloader as your hex file to upload.

On the Arduino dock 2, GPIO 19 of Omega2 is connected to the MCU_RESET circuit for software resetting the ATmega. Therefore, the 19 on the Expansion Header is grounded and should not be used for anything but ground. In addition, GPIO 19 on the Omega2 should be kept LOW or it will keep on resetting the MCU.

I have an Omega2plus and an Arduino dock v2. I have installed avrdude 6.1 and arduino-dock-2. I am unable to program the Atmega328 from the Omega2. I can attach a USBasp dongle to the arduino dock's six pin header and program the Atmega328, but cannot program it using the Omega2. I have followed what others have posted without success. When I open the arduino ide, select Tools, Board: Arduino/Genuino Uno the port does not change and no options for anything other than Port1 are displayed. What do I have to do to get the Omega2 to show up as a port (I tried restarting the daemon, does not work). Also, where in the Omega2's file system is the bootloader located and what is it's name ? I ask because using generic 'bootloader' comes back with no file found. The fuses were set, but no file named 'bootloader' could be found. BTW I am not an Arduino newbie. I am a Linux newbie, but learning.

On another note, I am very disappointed to receive the Omega2+ that I ordered, only to find out that the SD card slot that I paid extra for is non-functional and has no set date when it will be. Shame on Onion for selling vaporware.

@James-Behrens please see this post regarding the SD card: https://community.onion.io/topic/1282/omega2-reboot-and-sd-card-fixed
The SD card issue has been fixed. Onion has no intention of selling vaporware, not now, not ever. We have a track record of keeping all of our promises, we're a young company and still learning how to keep to our timelines. We appreciate everyone's patience and support as we're really trying to bring a useful product to the end users.

Please see the full Arduino Dock documentaiton for all of the steps: https://docs.onion.io/omega2-docs/flash-arduino-dock-wirelessly.html
You might have missed modifying the Arduino IDE boards.txt file, without this modification, the Arduino Dock will not show up as a port.
Also please make sure you're running avrdude v6.1-1, try running opkg list-installed | grep avrude to find the version info.

Not sure which bootloader you're trying to find on the Omega's filesystem?

I have an Omega2plus 0.1.7 b139 and an Arduino dock v2 0.1-1. I have installed avrdude 6.1-1 and modified the boards.txt. Even running opkg list-installed and find it still there. What ever I do today as it was working well yesterday between Onion Omega and Arduino IDE but not today, what going on?
Found it sometime worked most of the time don't work, think it the antenna kinda hit and miss depend how you place it. If it don't work move it somewhere not too far from the spot. Anyway you try.

I upgraded to firmware version 0.1.9 b149. The SD card is being recognized. Thank you for that.

I have read in the documentation how to transfer the file system to a flash drive attached to the USB port. Can I transfer the file system to the SD card ? I have done this with a competitor’s SOC that uses the same processor as the Omega. The file system on an SD card is better than using a flash drive. It makes for a more compact setup and an expansion dock is not required.

Back to the Arduino dock V2. With the new firmware I am able to flash the Atmega328 on the Arduino-dock V2. The omega finally shows up in the Arduino IDE’s port list.

How about publishing the actual schematic of the Arduino-dock V2. The current documentation has the schematic of the Arduino-doc V1.

I tried to burn the bootloader into the Atmega328 on the Arduino dock V2 by using the Linux command given in the documentation; “sh /usr/bin/Arduino-dock flash bootloader”. All this does is tell me the Omega cannot find “bootloader”. That is why I asked where the Arduino bootloader file can be found. I thought that “bootloader” was a stand-in for the real file name. Foolish me. Turns out the bootloader is not needed.

BTW My system had the Bonjour service installed and I still could not connect using “omega-xxxx.local” until I edited the Windows hosts file and added the IP address and host name. I also setup my router to provide a fixed IP for the Omega’s MAC address. Which is another issue. The paper label on the Omega has a MAC address on it, but it is not the same MAC address that the Omega’s WiFi is using. The MAC on the paper label is used by the br-wlan, eth0 and eth0.1. A different MAC is used by apcli0. I typed “ifconfig” to get this information. I used the apcli0 MAC to setup my router. Again, it would be nice if things worked as described in the documentation.@James-Behrens

0.1.9 b149 seems to have broken my ability to connect to my arduino wirelessly. After updating it looks like the packages were uninstalled. I reinstalled them (opkg update, opkg install arduino-dock-2), still can't see the device. Rebooted my arduino, nothing, rebooted my Mac laptop, still nothing. The boards.txt file is still modified. Any suggestions?
edit: pulling the power cord and rebooting the unit that way fixed it! Still, I'm curious why the packages were uninstalled after updating the firmware, I thought those were installed to root?